AFNI version info (afni -ver
): afni/21.3.04
Hello,
I am again struggling with running another script (this time afni_proc) on our system's new supercomputer. On our previous system, ROAR, we would execute the afni_proc script using "\. filename", but this doesn't seem to be working as I get the following error (see below). However, I do assign a subject number in the script and this same script worked on our previous systerm. Is there another way I need to execute this script? Or do you see anything else that should be modified? Any help would be much appreciated.
Thank you!
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\. updated_afni_proc.csh
** error: arg #1 (-subj_id) requires 1 params, found 0
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** failed command (get_user_opts):
afni_proc.py -subj_id -script proc. -scr_overwrite -copy_anat \
/anatSS.sub-951.nii -anat_has_skull no -dsets / -blocks tshift align \
tlrc volreg blur mask scale regress -radial_correlate_blocks tcat \
volreg -tcat_remove_first_trs 0 -align_opts_aea -cost lpc+ZZ \
-giant_move -check_flip -tlrc_base -tlrc_NL_warp -tlrc_NL_warped_dsets \
anatQQ.sub-951.nii anatQQ.sub-951.aff12.1D anatQQ.sub-951_WARP.nii \
-volreg_align_to MIN_OUTLIER -volreg_align_e2a -volreg_tlrc_warp \
-mask_epi_anat yes -blur_size 4.0 -regress_stim_times \
/LoseBig_FB_Correct.1D /LoseBig_FB_Error.1D /LoseSmall_FB_Correct.1D \
/LoseSmall_FB_Error.1D /WinBig_FB_Correct.1D /WinBig_FB_Error.1D \
/WinSmall_FB_Correct.1D /WinSmall_FB_Error.1D /Neutral_FB_Correct.1D \
/Neutral_FB_Error.1D /PunBig_Anticipation.1D /PunSmall_Anticipation.1D \
/WinBig_Anticipation.1D /WinSmall_Anticipation.1D \
/Neutral_Anticipation.1D -regress_stim_labels LB_FB_Correct LB_FB_Error \
LS_FB_Correct LS_FB_Error WB_FB_Correct WB_FB_Error WS_FB_Correct \
WS_FB_Error Neutral_FB_Correct Neutral_FB_Error PB_Anticipation \
PS_Anticipation WB_Anticipation WS_Anticipation Neutral_Anticipation \
-regress_basis_multi 'BLOCK(2)' 'BLOCK(2)' 'BLOCK(2)' 'BLOCK(2)' \
'BLOCK(2)' 'BLOCK(2)' 'BLOCK(2)' 'BLOCK(2)' 'BLOCK(2)' 'BLOCK(2)' \
dmBLOCK dmBLOCK dmBLOCK dmBLOCK dmBLOCK -regress_stim_types times times \
times times times times times times times times AM1 AM1 AM1 AM1 AM1 \
-regress_censor_motion 0.3 -regress_censor_outliers 0.05 \
-regress_motion_per_run -regress_opts_3dD -gltsym 'SYM: LB_FB_Correct \
-LB_FB_Error' -glt_label 1 LoseBig_FB_Correct-LoseBig_FB_Error -gltsym \
'SYM: LB_FB_Correct -LS_FB_Correct' -glt_label 2 \
LoseBig_FB_Correct-LoseSmall_FB_Correct -gltsym 'SYM: LB_FB_Error \
-LS_FB_Correct' -glt_label 3 LoseBig_FB_Error-LoseSmall_FB_Correct \
-gltsym 'SYM: 0.333*LB_FB_Correct +0.333*LB_FB_Error \
+0.333*LS_FB_Correct' -glt_label 4 mean.LLL -gltsym 'SYM: LB_FB_Correct \
-0.5*LB_FB_Error -0.5*LS_FB_Correct' -glt_label 5 L-LL \
-regress_3dD_stop -regress_reml_exec -regress_compute_fitts \
-regress_make_ideal_sum sum_ideal.1D -regress_est_blur_epits \
-regress_est_blur_errts -regress_run_clustsim no -html_review_style \
pythonic -execute
Below is a cleaner version of the script:
#!/usr/bin/env tcsh
# set data directories
set top_dir = /storage/group/qum17/default/anhedonia/tasks/MID/948
# set subject and group identifiers
set subj = s948
set group_id = g1
set basedset = MNI152_2009_template_SSW.nii.gz
# run afni_proc.py to create a single subject processing script
afni_proc.py \
-subj_id $subj \
-script proc.$subj -scr_overwrite \
-copy_anat $top_dir/anatSS.sub-948.nii \
-anat_has_skull no \
-test_stim_files no \
-dsets \
$top_dir/warped+orig.BRIK \
-blocks tshift align tlrc volreg blur mask scale regress \
-radial_correlate_blocks tcat volreg \
-tcat_remove_first_trs 0 \
-align_opts_aea -cost lpc+ZZ -giant_move -check_flip \
-tlrc_base $basedset \
-tlrc_NL_warp \
-tlrc_NL_warped_dsets \
anatQQ.sub-948.nii \
anatQQ.sub-948.aff12.1D \
anatQQ.sub-948_WARP.nii \
-volreg_align_to MIN_OUTLIER \
-volreg_align_e2a \
-volreg_tlrc_warp \
-mask_epi_anat yes \
-blur_size 4.0 \
-regress_stim_times \
$top_dir/LoseBig_FB_Correct.1D \
$top_dir/LoseBig_FB_Error.1D \
$top_dir/LoseSmall_FB_Correct.1D \
$top_dir/LoseSmall_FB_Error.1D \
$top_dir/WinBig_FB_Correct.1D \
$top_dir/WinBig_FB_Error.1D \
$top_dir/WinSmall_FB_Correct.1D \
$top_dir/WinSmall_FB_Error.1D \
$top_dir/Neutral_FB_Correct.1D \
$top_dir/Neutral_FB_Error.1D \
$top_dir/PunBig_Anticipation.1D \
$top_dir/PunSmall_Anticipation.1D \
$top_dir/WinBig_Anticipation.1D \
$top_dir/WinSmall_Anticipation.1D \
$top_dir/Neutral_Anticipation.1D \
-regress_stim_labels \
LB_FB_Correct LB_FB_Error LS_FB_Correct LS_FB_Error WB_FB_Correct WB_FB_Error WS_FB_Correct WS_FB_Error Neutral_FB_Correct Neutral_FB_Error PB_Anticipation PS_Anticipation WB_Anticipation WS_Anticipation Neutral_Anticipation \
-regress_basis_multi 'BLOCK(2)' 'BLOCK(2)' 'BLOCK(2)' 'BLOCK(2)' 'BLOCK(2)' 'BLOCK(2)' 'BLOCK(2)' 'BLOCK(2)' 'BLOCK(2)' 'BLOCK(2)' 'dmBLOCK' 'dmBLOCK' 'dmBLOCK' 'dmBLOCK' 'dmBLOCK' \
-regress_stim_types times times times times times times times times times times AM1 AM1 AM1 AM1 AM1 \
-regress_censor_motion 0.3 \
-regress_censor_outliers 0.05 \
-regress_motion_per_run \
-regress_opts_3dD \
-gltsym 'SYM: LB_FB_Correct -LB_FB_Error' \
-glt_label 1 LoseBig_FB_Correct-LoseBig_FB_Error \
-gltsym 'SYM: LB_FB_Correct -LS_FB_Correct' \
-glt_label 2 LoseBig_FB_Correct-LoseSmall_FB_Correct \
-gltsym 'SYM: LB_FB_Error -LS_FB_Correct' \
-glt_label 3 LoseBig_FB_Error-LoseSmall_FB_Correct \
-gltsym 'SYM: 0.333*LB_FB_Correct +0.333*LB_FB_Error +0.333*LS_FB_Correct' \
-glt_label 4 mean.LLL \
-gltsym 'SYM: LB_FB_Correct -0.5*LB_FB_Error -0.5*LS_FB_Correct' \
-glt_label 5 L-LL \
-regress_3dD_stop \
-regress_reml_exec \
-regress_compute_fitts \
-regress_make_ideal_sum sum_ideal.1D \
-regress_est_blur_epits \
-regress_est_blur_errts \
-regress_run_clustsim no \
-html_review_style pythonic \
-execute